Need to void a commission check from the vendor account and reissue to the sales person

I apologize if this is convoluted:

2 commission check were issued from a clients store account but they should have been issued from a different one.

We made the mistake of just voiding the 2 checks and reissued them out of the correct account but now we have a credit on the store account that needs to go away. How do I fix it and how should of it been done.